Supplementary Figure 1. Characterization of human carotid plaques. (a) Flash-frozen human plaques were separated into vulnerable (V) and stable (S),

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1 Supplementary Figure 1. Characterization of human carotid plaques. (a) Flash-frozen human plaques were separated into vulnerable (V) and stable (S), regions which were then quantified for mean fluorescence intensity (MFI) of DHE staining. t-test, **P<0.01, n = 8 donors; Scale bar, 100 µm. (b) The correlation of RvD1 and DHE levels in plaques. P = 0.011, n = 5 donors. (c-d) Comparison of 5-LOX-derived SPMs (RvD1 and LXA 4 ) and the SPM:LTB 4 ratio in vulnerable vs. stable regions from symptomatic plaques (c) vs. asymptomatic plaques (d). For (c) t-test, *P<0.05, n = 8 and for (d) n = 7 donors.

2 Supplementary Figure 2. Lipid mediators identified in stable and vulnerable regions of human carotid plaques. (a) Representative MS/MS spectra of RvD1, LTB 4, LXA 4, and LXB 4 identified in human atherosclerotic lesions. (b-d) Quantification of PGE 2, PGD 2, LXB 4 and 5-HETE; key eicosapentaenoic acid (EPA)-derived lipid mediators; and protectin D1 (PD1) in stable vs. vulnerable plaque regions (n = 15 donors). Data are shown as mean ± s.e.m., t-test, *P<0.05, n = 15 donors.

3 Supplementary Figure 3. Quantification of ROS, cleaved caspase 3, and 5-LOX signaling in human macrophages incubated with 7KC. (a) Human macrophages were pre-incubated with vehicle control (Veh) or 10 µm NAC for 1 h and then with Veh or 35 µm 7KC for 5 h. Reactive oxygen species were measured using the CellROX probe. Data are shown as mean ± s.e.m., Kruskal-Wallis

4 test, ***P<0.001 vs. all other groups, n = 3 separate donors. (b) Human macrophages were incubated with vehicle or 35 µm of 7KC for 5 h and then monitored for cleaved caspase 3 by flow cytometry. Shown is a representative histogram of 1 of 3 separate donors. (c) Human macrophages were incubated with vehicle (Veh), 10 nm RvD1 (D1), 35 µm 7KC, or RvD1 + 7KC (7KC + D1) for 3 h. CaMKII was immunoprecipitated from whole cell lysates, and the immunoprecipitates were then probed for methionine-oxidized CaMKII (oxcamkii) and total CaMKII by immunoblotting. A representative immunoblot is shown. Data shown are mean ± s.e.m., *P<0.05, n = 3 individual experiments from 3 separate donors. (d,e) Quantification of p-mk2 and p-5-lox-ser271 in macrophages incubated for 3 h with vehicle, 35 µm 7KC, 10 nm RvD1, or 7KC + RvD1. Data shown are mean ± s.e.m., *P<0.05, n = 3-4 separate donors; ns, non-significant. (f) Human macrophages were treated for 72 h with control sirna (sictrl) or Camk2g sirna (sicamkiiγ) and then subjected to flow cytometry to confirm knockdown. The left panel shows quantification of the flow data (mean ± s.e.m., ***P<0.001, n = 3 separate donors). The right panel is a representative flow cytometry histogram where gray is the IgG group, red is the sicamkiiγ group, and blue are sictrl group. (g) Human macrophages were treated for 72 h with control sirna (sictrl) or Camk2g sirna (sicamkii) and then incubated for 5 h with Veh, RvD1, 7KC, or 7KC + RvD1. Incubations were stopped with 4% formalin, and cells were permeabilized and subjected to anti-5-lox immunofluorescence confocal microscopy. Images were acquired on a Leica confocal microscope, and nuclear:non-nuclear 5-LOX MFI was quantified using Image J. Data are shown as mean ± s.e.m. (n = 4 separate donors). Statistical analysis was conducted using two-way ANOVA with Tukey multiple comparison test (**P<0.01, ***P<0.001 for sictrl 7KC vs. other treatments; ^^^P<0.001 for sictrl Veh vs. sictrl 7KC). (h) Human macrophages were incubated as in Fig 1e, and the media were assayed for RvD1 by ELISA. Data are shown as mean ± s.e.m. (n = 5 separate donors). Statistical analysis was conducted using two-way ANOVA with Tukey multiple comparison test (*P<0.01 for DHA vs. sictrl 7KC+DHA; ^^P<0.01, ^^^ P<0.001 for sictrl Veh vs. other treatments).

5 Supplementary Figure PGDH levels in human macrophages and murine lesions. (a) Human macrophages were incubated with 35 µm 7KC for 1, 3, or 5 h, and then cell lysates were subjected to immunoblot analysis for 15-PDGH and β-actin. Shown is a representative immunoblots image from one of two separate donors, with each time point carried out in triplicate. (b) Aortic root lesions of 17-week WD-fed Ldlr -/- mice treated with vehicle control (Veh) or RvD1 for weeks (see Fig. 3) were quantified for 15-PGDH MFI by immunofluorescence microscopy. Data are shown as mean ± s.e.m., t-test, n.s, not significant, n = 11 for Veh group and n = 10 for RvD1 group.

6 Supplementary Figure 5. Lesional lipid mediators after administration of RvD1 to WD-fed Ldlr -/- mice with established atherosclerosis. (a-c) Aortic root lesions of 17-week WD-fed Ldlr -/- mice given vehicle control (Veh) or RvD1 for weeks (see Fig. 3) were quantified for the 12- and 15- LOX-derived products protectin D1 (PD1), 17-HDHA, 15-HETE, and maresin 1 (MaR1); cyclooxygenase-derived prostaglandins PGF 2α, PGE 2, and PGD 2 ; and the 5-LOX-generated monohydroxy products 5-HETE, 5-HEPE, 4-HDHA, and 7-HDHA. Data are shown as mean ± s.e.m., t-test, *P<0.05, n = 11 for Veh group and n = 10 for RvD1 group.

7 Supplementary Figure 6. Gallery of nuclear 5-LOX in aortic lesional macrophages. Aortic root sections were sequentially incubated with anti-5-lox antibody overnight at 4oC followed by antif4/80 for 2 h at room temperature. Sections were counterstained with Hoechst and analyzed using a Nikon A1 confocal microscope and ImageJ software. Images display F4/80 in red, 5-LOX in green, and Hoechst in blue. Nuclei are outlined by a hashed line, and individual macrophages are outlined by a solid line. Scale bar, 5 µm.

8 Supplementary Figure 7. Systemic and metabolic parameters and local cell counts in Ldlr -/- mice treated with Veh or RvD1. (a-c) Body weight, plasma cholesterol levels, and plasma insulin levels, in 17-week WD-fed Ldlr -/- mice given vehicle control (Veh) or RvD1 for weeks (see Fig. 3). (d) Plasma levels of MCP-1 in Veh vs. RvD1 groups were analyzed by ELISA. (e,f) Macrophage and smooth muscle cells numbers in lesions were quantified by immunofluorescence and image processing. Data are shown as mean ± s.e.m., t-test, n.s., not significant, n = 11 for Veh group and n = 10 for RvD1 group.

9 Supplementary Figure 8. Gallery of images from in-situ efferocytosis analysis of lesions of Ldlr-/- mice treated with Veh or RvD1. (a) In situ efferocytosis analysis, as described in Supplementary Methods, was conducted on aortic root sections from 17-week WD-fed Ldlr-/- mice given vehicle control (Veh) or RvD1 for weeks (see Fig. 3). The macrophage marker F4/80 is shown in green, apoptotic cells (ACs) are shown in red, and nuclei are shown in blue. White arrows indicate free apoptotic cells, and white asterisks indicate associated ACs. Scale bar, 10 µm. (b) Quantification of total ACs per lesion. Data are shown as mean ± s.e.m., n.s., not significant, n = 11 for Veh group and n = 10 for RvD1 group.

10 Supplementary Table 1. Clinical characteristics of patients who underwent an elective endarterectomy. Demographics Age, yr (mean ± SEM) 69 ± 2.4 Male 13/15 Female 2/15 Anthropometrics Body weight, kg (mean ± SEM) 87 ± 4.2 Height, m (mean ± SEM) 1.8 ± 0.02 BMI (mean ± SEM) 28 ± 1.1 CVD risk factors and clinical classification of carotid lesions Smoking 3/15 Diabetes 5/15 Asymptomatic 7/15 Symptomatic 8/15 Aspirin and Statin use Aspirin 15/15 Statin 12/15

11 Supplementary Table 2. Human plaque and mouse aorta specimen weights used for LC-MS/MS. Human plaques (g) Stable (n=15) Vulnerable (n=15) 0.08 ± ± 0.06 Mouse aorta (mg) Early (n=8) Advanced (n=11) 9.41 ± ± 1.03 Data are mean ± s.e.m.

12 Supplementary Table 3. Quantification of docosahexaenoic acid-derived lipid mediators in aortic lesions of Ldlr -/- mice fed the WD for 8 weeks (Early Lesions) or 17 weeks (Advanced Lesions), with either Vehicle or RvD1 administered during weeks Lipid Mediator Early Lesion pg/g (mean ± SEM) Advanced Lesion-Vehicle pg/g (mean ± SEM) Docosahexaenoic acid-derived Advanced Lesion-RvD1 pg/g (mean ± SEM) 4-HDHA ± ± 22.7* ± HDHA 76.3 ± ± 7.1* 62.4 ± HDHA 91.0 ± ± 10.3* ± HDHA 65.6 ± ± 25.8* ± 28.8 PD ± ± 1.3* 9.3 ± 1.5 Mar ± ± ± 42.4 RvD ± ± 1.2* 40.6 ± 12.2 RvD2 ND ND ND RvD3 ND ND ND RvD4 ND ND ND RvD5 ND ND ND RvD6 ND ND ND 17R-RvD ± ± 86.1* ± OH-PD1 ND ND ND 13-HDHA ± ± 26.9* ± R-RvD3 ND ND ND 4S,14S-diHDHA ND ND ND Δ12-trans-MaR1 ND ND ND 7-epi,Δ12-trans-MaR1 ND ND ND *= P< 0.05 (Early vs. Advanced Lesion-Vehicle); = P< 0.05 (Advanced Lesion-Vehicle vs. Advanced Lesion-RvD1). ND stands for not detected.

13 Supplementary Table 3 cont. Quantification of Arachidonic acid-derived lipid mediators in aortic lesions of Ldlr -/- mice fed the WD for 8 weeks (Early Lesions) or 17 weeks (Advanced Lesions), with either Vehicle or RvD1 administered during weeks Lipid Mediator Early Lesion pg/g (mean ± SEM) Advanced Lesion- Vehicle pg/g (mean ± SEM) Arachidonic acid-derived Advanced Lesion-RvD1 pg/g (mean ± SEM) 5-HETE ± ± ± HETE ± ± 572.9* ± HETE ± ± ± ,15-diHETE ± ± 144.4* ± PGD ± ± 32.2* ± 80.3 PGE ± ± 34.5* ± 36.4 PGF 2α 45.2 ± ± 11.3* ± R-LXA ± ± 25.2* ± 34.9 LTB ± ± ± 2.6 Δ6-trans-LTB ± ± 1.3* 28.1 ± epi-Δ6-trans- LTB ± ± ± OH-LTB 4 ND ND ND 20-COOH-LTB 4 ND ND ND 11-HETE ± ± ± S-6R-diHETE ND ND ND LXB ± ± 13.7* 80.5 ± 28.6 LXA 4 ND ND ND *= P< 0.05 (Early vs. Advanced Lesion-Vehicle); = P< 0.05 (Advanced Lesion-Vehicle vs. Advanced Lesion-RvD1). ND stands for not detected.

14 Supplementary Table 3 cont. Quantification of Eicosapentaenoic acid- acid-derived lipid mediators in aortic lesions of Ldlr -/- mice fed the WD for 8 weeks (Early Lesions) or 17 weeks (Advanced Lesions), with either Vehicle or RvD1 administered during weeks Lipid Mediator Early Lesion pg/g (mean ± SEM) Advanced Lesion- Vehicle pg/g (mean ± SEM) Eicosapentaenoic Acid derived Advanced Lesion- RvD1 pg/g (mean ± SEM) 5-HEPE 40.7 ± ± 3.7* 28.2 ± HEPE ± ± ± HEPE 15.9 ± ± ± 14.7 RvE1 ND ND ND RvE2 ND ND ND RvE3 ND ND ND 5S,15SdiHEPE ND ND ND LXA 5 ND ND ND PGE 3 ND ND ND *= P< 0.05 (Early vs. Advanced Lesion-Vehicle); = P< 0.05 (Advanced Lesion-Vehicle vs. Advanced Lesion-RvD1). ND stands for not detected.